5TDJ

RNA decamer duplex with four 2'-5'-linkages


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into RNA duplexes with multiple 2 -5 -linkages.

Shen, F.Luo, Z.Liu, H.Wang, R.Zhang, S.Gan, J.Sheng, J.

(2017) Nucleic Acids Res. 45: 3537-3546

  • DOI: 10.1093/nar/gkw1307
  • Primary Citation of Related Structures:  5TDK

  • PubMed Abstract: 
  • 2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and st ...

    2΄-5΄-linked RNAs play important roles in many biological systems. In addition, the mixture of 2΄-5΄ and 3΄-5΄ phosphodiester bonds have emerged as a plausible structural element in prebiotic RNAs. Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones, we recently reported two crystal structures of a decamer RNA duplex containing two and six 2΄-5΄-linkages, showing how RNA duplexes adjust the structures to accommodate these non-canonical linkages (Proc. Natl. Acad. Sci. USA, 2014, 111, 3050-3055). Herein, we present two additional high-resolution crystal structures of the same RNA duplex containing four and eight 2΄-5΄-linkages at different positions, providing new insights into the effects of these modifications and a dynamic view of RNA structure changes with increased numbers of 2΄-5΄-linkages in the same duplex. Our results show that the local structural perturbations caused by 2΄-5΄ linkages can be distributed to nearly all the nucleotides with big ranges of changes in different geometry parameters. In addition, hydration pattern and solvation energy analysis indicate less favorable solvent interactions of 2΄-5΄-linkages comparing to the native 3΄-5΄-linkages. This study not only promotes our understanding of RNA backbone flexibility, but also provides a knowledge base for studying the biochemical and prebiotic significance of RNA 2΄-5΄-linkages.


    Organizational Affiliation

    Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')A,B10unidentified
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR
Query on SR

Download SDF File 
Download CCD File 
B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 27.538α = 90.00
b = 94.455β = 111.19
c = 21.283γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-09-19 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Luo, Z., Sheng, J.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Advisory, Data collection